Change the distance to transcript for which VEP assigns upstream and downstream consequences

5000

-

domains

Boolean

Include names of overlapping protein domains

0

-

failed

Boolean

When checking for co-located variants, by default variants flagged as failed by Ensembl's QC pipeline will be excluded. Set this flag to 1 to include such variants

0

-

hgvs

Boolean

Include HGVS nomenclature based on Ensembl stable identifiers

0

-

merged

Boolean

Use merged Ensembl and RefSeq transcript set to report consequences (human only)

0

-

miRNA

Boolean

Determines where in the secondary structure of a miRNA a variant falls (plugin details)

0

-

minimal

Boolean

Convert alleles to their most minimal representation before consequence calculation i.e. sequence that is identical between each pair of reference and alternate alleles is trimmed off from both ends, with coordinates adjusted accordingly. Note this may lead to discrepancies between input coordinates and coordinates reported by VEP relative to transcript sequences

0

-

numbers

Boolean

Include affected exon and intron positions within the transcript

0

-

protein

Boolean

Include Ensembl protein identifiers

0

-

refseq

Boolean

Use RefSeq transcript set to report consequences (human only)

0

-

transcript_id

String

Filter results by Transcript ID

Not Used

-

tsl

Boolean

Include transcript support level (TSL) annotation

0

-

uniprot

Boolean

Include best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc)

0

-

variant_class

Boolean

Output the Sequence Ontology variant class for the input variant

0

-

xref_refseq

Boolean

Include aligned RefSeq mRNA identifiers for transcript. NB: theRefSeq and Ensembl transcripts aligned in this way MAY NOT, AND FREQUENTLY WILL NOT, match exactly in sequence, exon structure and protein product